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- PDB-1gaf: 48G7 HYBRIDOMA LINE FAB COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL... -

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Basic information

Entry
Database: PDB / ID: 1gaf
Title48G7 HYBRIDOMA LINE FAB COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID
Components(CHIMERIC 48G7 FAB) x 2
KeywordsCATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID / : / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsWedemayer, G.J. / Patten, P.A. / Stevens, R.C. / Schultz, P.G.
Citation
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: A Genetic Approach to the Generation of Antibodies with Enhanced Catalytic Activities
Authors: Lesley, S.A. / Patten, P.A. / Schultz, P.G.
History
DepositionFeb 6, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CHIMERIC 48G7 FAB
H: CHIMERIC 48G7 FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9963
Polymers46,6942
Non-polymers3021
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-22 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.260, 44.850, 85.450
Angle α, β, γ (deg.)90.00, 121.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody CHIMERIC 48G7 FAB


Mass: 23485.045 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS
Source method: isolated from a genetically manipulated source
Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY ...Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY CHAIN CONSISTS OF THE VDJ VARIABLE DOMAIN FROM MOUSE AND THE C(H1) CONSTANT REGION FROM HUMAN
Source: (gene. exp.) Homo sapiens (human)
Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE
Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Production host: BL21 / References: GenBank: 4768677, UniProt: P01834*PLUS
#2: Antibody CHIMERIC 48G7 FAB


Mass: 23209.020 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS
Source method: isolated from a genetically manipulated source
Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY ...Details: BOTH FAB CHAINS ARE DERIVED FROM THE MATURE (HYBRIDOMA LINE) ANTIBODY. THE LIGHT CHAIN CONSISTS OF THE VJ VARIABLE DOMAIN FROM MOUSE AND THE C(KAPPA) CONSTANT REGION FROM HUMAN. THE HEAVY CHAIN CONSISTS OF THE VDJ VARIABLE DOMAIN FROM MOUSE AND THE C(H1) CONSTANT REGION FROM HUMAN
Source: (gene. exp.) Homo sapiens (human)
Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE
Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Production host: BL21 / References: UniProt: P01857
#3: Chemical ChemComp-NPE / 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID


Mass: 302.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 44.8 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/ml48G7 Fab11
21 mMhapten11
3100 mMsodium acetate11
4100 mMsodium cacodylate11
527 %PEG330011

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 33282 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Num. measured all: 121262

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.95→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.307 -
Rwork0.244 -
obs0.244 33282
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 20 151 3453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.613
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3076
Solvent computation
*PLUS
Displacement parameters
*PLUS

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